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However if i use phpinfo() to display php info it says it is version 4.1.1 I know it is 4.2.2 since i copied the files there myself just to check.

Some pages will work and some will give server 500 errors. The paths seem to be wrong as relative links in files such as /site/includes/dbconnect.php are correct (worked before upgrade) but now give errors.

Any idea's? I'm downloading another package called Foxserv but maybe old config files left else where are conflicting.

Actually, if you copy the data structure that you have into the data folder of the new mysql install and restart mysql, you'll see all your databases in phpmyadmin.

I mean: in the data folder(that you backed-up), you have other folders (mysql, test and others if you created other databases). These folders must be copied in the data folder of the new install. I did that and it worked.